In a post-apocalyptic society, much of earthquake-riddled Japan has been left to ruin, resulting in an abundance of greenery. Governments manage much of the world's emissions, resulting in a massive class divide and economic disparity. The Japanese government launches "Project Atlas," a utopian city that will replace Tokyo but can only fit a certain amount of people. This limitation means that some people will have to live outside the city in jungles, as refugees. However, with any flawed plan comes those who are willing to challenge it. These include Kuniko Houjou, an heir to a renegade town; Mikuni, a mysterious and powerful child kept in a secret temple; Kunihito Kusanagi, a soldier for the high-tech and exclusive monopoly Atlas; Karin Ishida, a genius economics whiz with her hand in markets across the world; and the villainous Ryouko Naruse, leading Atlas in its domination of this future world. Can this group of rebels, forming a movement known as "Metal-Age," band together to demonstrate that inclusion and teamwork prevail over cruel segregation? [Written by MAL Rewrite]

The story revolves around Maya, the daughter of the former Headmaster of Waldstein Academy, and a time traveling agent Fumiaki Uchida. In the year 2012, the world had been invaded by aliens and time travelers were sent back to the year 1999 in order to find and destroy the Nostradamus Key, which Nostradamus Prophecy foretold as what would bring about the apocalypse. The series then turns to the year 1999, where Maya returns to the Academy with the intention of destroying the Academy by superseding her late father's position as the principal. Her plan was interrupted when she meets Fumiaki and learns of the forthcoming destruction. Despite being distrusting towards Fumiaki, they form a pact to look for the Nostradamus Key. In order to find the Nostradamus Key, time agents were provided with specially created cell phones. When a user finds an object of interest, by thinking of destroying it and taking a photo, and if the resulting image is that of a peaceful world, then the subject is the Nostradamus Key. Conversely, if the subject is not the Nostradamus Key, then the photo displays destruction. By using the phone, Maya and Fumiaki investigates occult occurrences as they occur in the town. (Source: Wikipedia)

In the year 2201, one year after the Yamato saved Earth from radioactive contamination, a new threat emerges. The Yamato makes its final journey to save the Earth from this new threat. Earth has almost recovered from the battle against Gamilus, and reconstruction has expanded to the other planets. When former Yamato crew-mates discover a strange, garbled message that seems to be coming from a white comet headed towards Earth, they hijack their old space fortress and begin a new battle.

Bean Bandit and his partner Rally Vincent are couriers for hire - transporting clients and delivering goods in his custom sports car "Roadbuster" for a hefty price. But when they are hired to escort a kidnapped girl named Chelsea to her home, they don't realize they're being framed for kidnapping as their former clients Semmerling and Carrie plan their escape with Chelsea's father and the ransom money.